The long-term goal this research program generates paradigms for how the ubiquitin-proteasome system (UPS) regulates transcription. Recent evidence has shown that components of the UPS are involved- directly and mechanistically-in numerous transcription-centric events such as gene activation, co-activator recruitment, histone function, co-transcriptional mRNA processing, and transcriptional termination. Yet the underlying molecular mechanisms at work, and the relationship between proteolytic versus non-proteolytic functions of the UPS in this context, remain obscure. To understand the fundamental ways in which ubiquitin (Ub), Ub-ligases, and the proteasome can influence general transcriptional processes, this project focuses on exposing how transcriptional activators are controlled by Ub-mediated proteolysis (proteolytic), how RNA polymerase II is regulated by non-proteolytic ubiquitylation, and how the proteasome regulates transcriptional events in the nucleus. These studies take advantage of the experimental tractability of the yeast Saccharomyces cerevisiae, and employ cutting-edge genetic, biochemical, proteomic, and genomic approaches to define both the mechanism and significance of control of transcription by the UPS. Results of these studies will have broad impact in two main areas. First, they will illuminate a poorly understood aspect of eukaryotic gene control. It has only recently been appreciated that the UPS is directly involved in transcriptional regulation, and although this is a rapidly evolving field, general themes and processes have yet to be defined. These studies will define these general themes, and in so doing reveal novel ways in which gene activity is regulated. Given the large number of oncogene transcription factors that are controlled by the UPS, results of this work are also likely to impact our understanding of diseases such as cancer. Second, this research will reveal how components of the UPS select their substrates and how they are recruited into distinct biological processes. An emerging theme in this project is that th UPS can 'sense' the activity of transcription proteins and interfaces directly with core components of the transcriptional machinery to modulate their activity. Understanding how the UPS does this within the context of transcription thus has significance for understanding how it integrates itself into various events within the cell. As the UPS plays a prominent role in cellula homeostasis and is dysregulated in a wide spectrum of diseases (from neurological disorders through to cancer), results of these studies will also have broad impact beyond the immediate field of gene regulation. PUBLIC HEALTH RELEVANCE: Regulation transcription and control proteins by the ubiquitin-proteasome system (UPS) are two processes that feature prominently in human disease. This research program explores an unexpected connection between these processes that play an important role in the control of gene activity. Results of these studies will provide paradigms for how the UPS impacts transcription in normal and disease states.